# Cannot generate summary plot

**URL:** <https://forum.biobakery.org/t/cannot-generate-summary-plot/8721>\
**Category:** MaAsLin\
**Created:** [January 20, 2026, 1:15pm UTC](https://forum.biobakery.org/t/cannot-generate-summary-plot/8721 "2026-01-20T13:15:47Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![WedwardsKent](https://avatars.discourse-cdn.com/v4/letter/w/c67d28/32.png) [@WedwardsKent](https://forum.biobakery.org/u/WedwardsKent)\
**Post date:** [January 20, 2026, 1:15pm UTC](https://forum.biobakery.org/t/cannot-generate-summary-plot/8721/1 "2026-01-20T13:15:47Z")

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Hello, i am working with a set of microbiome data from livestock. I have used maaslin3 to look for taxa associated with my experimental variable (for this post referred to as ‘red’ apologies, this data is still unpublished). i used the following formula

~red + green (1|blue)  
maaslin ran as intended and in the output i can see a summary plot and association plots for my ‘red’ variable. in the significant\_results.tsv i can see the following

 ![maaslin3query](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/2X/b/b64d72e2e35edf612b2da2be5fb8bd17c86bfea0.jpeg)

(here the red rows indicate taxa with red positive). I can see i have significant results, however when i try and remake the summary plot to only include my experimental variable, only the association plots are available, i do not get a summary plot.

sig\_plot\_data\<-maaslin3::maaslin\_plot\_results\_from\_output(  
output = “mas3.output”,  
metadata = maslin.meta\_data.s,  
normalization = “TSS”,  
transform = “LOG”,  
summary\_plot\_first\_n = 20,  
coef\_plot\_vars = c(“RedPositive”,“RedNegative”),  
heatmap\_vars = c(“RedPositive”,“RedNegative”),  
plot\_summary\_plot = TRUE  
)  
sig\_plot\_data$ only association plots not summary

apologies if this is clearly a rookie error but any help is really appreciated!

kindest regards

Will

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**Author:** ![WillNickols](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/willnickols/32/3223_2.png) [@WillNickols](https://forum.biobakery.org/u/WillNickols)\
**Post date:** [January 22, 2026, 5:32pm UTC](https://forum.biobakery.org/t/cannot-generate-summary-plot/8721/2 "2026-01-22T17:32:42Z")

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Do you mind posting the full running log or emailing me willnickols@g.harvard.edu if you don’t want it public? Usually it says towards the end why it didn’t generate the summary plot. It’s almost always an issue with the `coef_plot_vars` and `heatmap_vars` naming, and the log will tell you what the valid options are based on your data.

Will

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**Author:** ![WedwardsKent](https://avatars.discourse-cdn.com/v4/letter/w/c67d28/32.png) [@WedwardsKent](https://forum.biobakery.org/u/WedwardsKent)\
**Post date:** [January 23, 2026, 3:13pm UTC](https://forum.biobakery.org/t/cannot-generate-summary-plot/8721/3 "2026-01-23T15:13:45Z")

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Hi Will

you are correct! i was able to get a summary plot to generate once i had more accurately specified the heat and coef variables!

However it did bring up another quick question. I have five taxa for which i was able to generate a summary plot and association plots. When i look at significant\_results.tsv, i see a lot of taxa that are significant q-values, but dont have association plots?

Apologies again if these are just very rookie errors  
-Will

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**Author:** ![WillNickols](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/willnickols/32/3223_2.png) [@WillNickols](https://forum.biobakery.org/u/WillNickols)\
**Post date:** [January 23, 2026, 5:26pm UTC](https://forum.biobakery.org/t/cannot-generate-summary-plot/8721/4 "2026-01-23T17:26:05Z")

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Do you have `max_pngs` set to the default 30? If you bump that up to 1000, are they all there?